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I guess you are using the Toolbox in Production mapping to create your MEF Values.
I would look at the MEF Quadrants that have differences ie say 6500 ft vs 6400 ft. Where there are differences you may want to consider flight safety aspects and the users of the JOG-Air etc. So in The case above you would use 6500 ft, that way the safety margin is increased slighty.
The Mil standard (MIL-J-89100) and (MIL-T-89101) do explain calcs you need for the MEF. I would have a look at Section 3.14.1 in Mil-T-89101. It explains the rounding and vertical errors quite well. Also look here: